Done.
-parsing GTF file: /tmp/nxf.ULdfDeyq3O/tih_rna_sample_00124_B23WHTKLT4_2.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.ULdfDeyq3O/ctat_genome_lib_build_dir/ref_genome.fa.star.idx  --outSAMtype BAM SortedByCoordinate  --twopassMode None  --alignSJDBoverhangMin 10  --genomeSuffixLengthMax 10000 --limitBAMsortRAM 47271261705  --alignInsertionFlush Right   --alignMatesGapMax 100000  --alignIntronMax 100000  --outSAMattributes All  --readFilesIn /tmp/nxf.ULdfDeyq3O/tih_rna_sample_00124_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.ULdfDeyq3O/tih_rna_sample_00124_B23WHTKLT4_2_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.ULdfDeyq3O/fi_workdir/tih_rna_sample_00124_B23WHTKLT4_2.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.ULdfDeyq3O/fi_workdir/tih_rna_sample_00124_B23WHTKLT4_2.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00124_B23WHTKLT4_2.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00124_B23WHTKLT4_2.star.sortedByCoord.out.bam
10:34:13 : INFO : Done.
-parsing GTF file: /tmp/nxf.ULdfDeyq3O/fi_workdir/tih_rna_sample_00124_B23WHTKLT4_2.gtf
-parsing /tmp/nxf.ULdfDeyq3O/fi_workdir/tih_rna_sample_00124_B23WHTKLT4_2.star.cSorted.dupsMarked.bam

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[800000]   -done parsing /tmp/nxf.ULdfDeyq3O/fi_workdir/tih_rna_sample_00124_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'exons hit < 2' => 15,
          'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 2,
          'seq-similar region overlap' => 86,
          'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 5,
          'num_hits: 7 != num_counted_on_fusion_contigs 4 ' => 12,
          'per_id < 96' => 2429,
          'num genes matched < 2' => 58,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 5172,
          'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 1132,
          'num_hits: 7 != num_counted_on_fusion_contigs 5 ' => 5,
          'low complexity anchor region' => 3,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 3,
          'num_hits: 7 != num_counted_on_fusion_contigs 6 ' => 6,
          'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 284,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 2932,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 27,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 276,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 1854,
          'excessive soft clipping' => 4565,
          ' ** passed ** ' => 1439,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 2554,
          'small anchor length' => 4,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 1192
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.ULdfDeyq3O/fi_workdir/tih_rna_sample_00124_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[5000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

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[88000]   -fusion SPANNING read extraction for scaff: ANKRD30A--ARL6IP1P2

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[12000]   -fusion SPANNING read extraction for scaff: BLCAP--SEZ6

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[47000]   -fusion SPANNING read extraction for scaff: C6orf89--DDR1

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[40000]   -fusion SPANNING read extraction for scaff: DDX11--IPO8

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[15000]   -fusion SPANNING read extraction for scaff: KLRC4--KLRK1

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[102000]   
[103000]   -fusion SPANNING read extraction for scaff: NF1--TMEM161A

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[56000]   -fusion SPANNING read extraction for scaff: PILRA--PILRB

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[134000]   -fusion SPANNING read extraction for scaff: PLEKHM1--MAP4K4

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[47000]   -fusion SPANNING read extraction for scaff: RIC1--INSL4

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[61000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[23000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[4000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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[11000]   -fusion SPANNING read extraction for scaff: TPST1--AC073210.1

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[18000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[122000]   -fusion SPANNING read extraction for scaff: XRN1--ATR

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[13000]   -fusion SPANNING read extraction for scaff: ZNF692--GCSAML
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 24570,
          'lacks exon overlap' => 8636
        };
EM: Starting log likelihood: -2165.317460
EM: Round [1] log likelihood: -2165.081052
EM: Round [2] log likelihood: -2165.080230
EM: Round [3] log likelihood: -2165.080222
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.ULdfDeyq3O/tih_rna_sample_00124_B23WHTKLT4_2.consolidated.bam into /tmp/nxf.ULdfDeyq3O/tih_rna_sample_00124_B23WHTKLT4_2.consolidated.bam.read_coords

CMD: touch /tmp/nxf.ULdfDeyq3O/tih_rna_sample_00124_B23WHTKLT4_2.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.ULdfDeyq3O/tih_rna_sample_00124_B23WHTKLT4_2.consolidated.bam.read_coords > /tmp/nxf.ULdfDeyq3O/tih_rna_sample_00124_B23WHTKLT4_2.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.ULdfDeyq3O/tih_rna_sample_00124_B23WHTKLT4_2.consolidated.bam.frag_coords > /tmp/nxf.ULdfDeyq3O/tih_rna_sample_00124_B23WHTKLT4_2.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.ULdfDeyq3O/fi_workdir/tih_rna_sample_00124_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.ULdfDeyq3O/fi_workdir/tih_rna_sample_00124_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter  --genome_lib_dir ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 50 
CMD: cp /tmp/nxf.ULdfDeyq3O/fi_workdir/tih_rna_sample_00124_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.ULdfDeyq3O/tih_rna_sample_00124_B23WHTKLT4_2.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.ULdfDeyq3O/tih_rna_sample_00124_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -2107.458209
EM: Round [1] log likelihood: -2107.221801
EM: Round [2] log likelihood: -2107.220979
EM: Round [3] log likelihood: -2107.220971
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.ULdfDeyq3O/tih_rna_sample_00124_B23WHTKLT4_2_1.fastp.fastq.gz: 225028134
Warning - not locating file: /tmp/nxf.ULdfDeyq3O/tih_rna_sample_00124_B23WHTKLT4_2.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000227113.2]
WARNING, no entry stored in dbm for [ENSG00000227113.2]
ls: cannot access 'IGV_inputs': No such file or directory